Through the work of many groups, fluconazole resistance in some, but not all clinical isolates has been associated with the gene target of the drug, ERG11, as well as genes for cellular pumps, CDR1, CDR2 and MDR1. The mechanisms implicating these genes in resistance are not fully understood, and it is uncertain that the entire repertoire of fluconazole genes have been identified. In our recent work, we showed for the first time that under laboratory condition 10 independent fluconazole resistant mutants that derived after a short exposure of one week to the drug, all lost a copy of chromosome 4. The mRNA level of the above mentioned genes in these mutants was not changed. A total of 7 independent fluconazole resistant mutants that derived after at least one month of exposure to the drug, all possessed the diminution of chromosome 4, and acquired a second specific change, an extra-copy of chromosome 3. Consistently, the expression of the gene CDR1, which is carried on the duplicated chromosome, but not of the other genes, was increased. Our results are remarkably similar to the published data describing series of C. albicans sequentially isolated clinical strains with a progressive increase of resistance over time, which did not initially show or did not have any mutations or overexpression of the genes associated with the resistance. We propose to test our hypothesis that the primary response of clinical isolates to fluconazole is specific changes in chromosomal copy number. The higher resistance levels of later clinical isolates can be viewed as secondary changes, which occur as a result of accumulation of gene mutations under prolonged selective pressure. We developed special procedure to isolate and handle C. albicans series of sequential genetically related strains from patients undergoing fluconazole treatment, thus protecting the isolates from stresses other than action of fluconazole, which can induce undesirable chromosomal instability. The reliable series of strains will be characterized for their electrophoretic karyotypes. If the change in copy number of a specific chromosome(s) is/are observed with clinical samples resistant to fluconazole, we are in the position to further study the still unknown genes responsible for this novel mechanism of resistance.